4A25 - JenaLib

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Title :   X-RAY STRUCTURE DPS FROM KINEOCOCCUS RADIOTOLERANS IN COMPLEX WITH MN (II) IONS.

Authors :   A. Ilari, A. Fiorillo, M. Ardini, S. Stefanini, E. Chiancone

Date :   22 Sep 11 (Deposition) - 03 Oct 12 (Release) - 15 May 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D  (3x)

Keywords :   Metal Binding Protein, Detoxification Process (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Ardini, A. Fiorillo, M. Fittipaldi, S. Stefanini, D. Gatteschi, A. Llari, E. Chiancone
Kineococcus Radiotolerans Dps Forms A Heteronuclear Mn-Fe Ferroxidase Center That May Explain The Mn-Dependent Protection Against Oxidative Stress.
Biochim. Biophys. Acta V. 1830 3745 2013
PubMed-ID: 23396000 | Reference-DOI: 10.1016/J.BBAGEN.2013.02.003

Molecule 1 - FERRITIN DPS FAMILY PROTEIN
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector	:	PET-11A
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 2-170
	Organism Scientific	:	KINEOCOCCUS RADIOTOLERANS
	Organism Taxid	:	131568
	Synonym	:	DPS

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (3x)	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 16)

No.	Name	Count	Type	Full Name
1	CL	6	Ligand/Ion	CHLORIDE ION
2	MN	10	Ligand/Ion	MANGANESE (II) ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	MN	-1	Ligand/Ion	MANGANESE (II) ION

Asymmetric Unit (16, 16)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASP A:75 , GLU A:79 , HOH A:2045 , HOH A:2052 , HIS B:48	BINDING SITE FOR RESIDUE MN A1169
02	AC2	SOFTWARE	ASP A:144 , MN A:1171 , HOH A:2073 , HOH A:2075 , HOH A:2087 , ASP B:144 , ASP C:144	BINDING SITE FOR RESIDUE MN A1170
03	AC3	SOFTWARE	ASP A:144 , HIS A:147 , MN A:1170 , HOH A:2074 , HOH A:2076 , ASP B:144 , ASP C:144	BINDING SITE FOR RESIDUE MN A1171
04	AC4	SOFTWARE	ASN A:55 , ASP A:58	BINDING SITE FOR RESIDUE MN A1172
05	AC5	SOFTWARE	LYS A:45 , ARG A:71 , ARG B:71	BINDING SITE FOR RESIDUE CL A1173
06	AC6	SOFTWARE	ARG A:57 , HOH A:2030	BINDING SITE FOR RESIDUE CL A1174
07	AC7	SOFTWARE	HIS A:48 , HOH A:2023 , HOH A:2025 , ASP B:75 , GLU B:79	BINDING SITE FOR RESIDUE MN B1171
08	AC8	SOFTWARE	ASN B:55 , ASP B:58 , ASN C:55 , ASP C:58 , ASN D:55 , ASP D:58	BINDING SITE FOR RESIDUE MN B1172
09	AC9	SOFTWARE	ARG A:71 , LYS B:45 , ARG B:71	BINDING SITE FOR RESIDUE CL B1173
10	BC1	SOFTWARE	ARG B:57 , HOH B:2020 , ARG C:57 , ARG D:57	BINDING SITE FOR RESIDUE CL B1174
11	BC2	SOFTWARE	ASP C:75 , GLU C:79 , HOH C:2046 , HOH C:2053 , HIS D:48	BINDING SITE FOR RESIDUE MN C1171
12	BC3	SOFTWARE	LYS C:45 , ARG C:71 , ARG D:71	BINDING SITE FOR RESIDUE CL C1172
13	BC4	SOFTWARE	HIS C:48 , HOH C:2024 , HOH C:2026 , ASP D:75 , GLU D:79	BINDING SITE FOR RESIDUE MN D1169
14	BC5	SOFTWARE	ASP D:144 , MN D:1171 , HOH D:2060	BINDING SITE FOR RESIDUE MN D1170
15	BC6	SOFTWARE	ASP D:144 , MN D:1170 , HOH D:2059	BINDING SITE FOR RESIDUE MN D1171
16	BC7	SOFTWARE	ARG C:71 , LYS D:45 , ARG D:71	BINDING SITE FOR RESIDUE CL D1172

(no "SS Bond" information available for 4A25)

(no "Cis Peptide Bond" information available for 4A25)

(no "SAP(SNP)/Variant" information available for 4A25)

(no "PROSITE Motif" information available for 4A25)

(no "Exon" information available for 4A25)

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:167
 aligned with A6WG04_KINRD | A6WG04 from UniProtKB/TrEMBL  Length:170

    Alignment length:167
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       
         A6WG04_KINRD     2 TTIHDVQTTGLTQDAVTGFDASSRLNAGLQEVLVDLTALHLQGKQAHWNIVGENWRDLHLQLDTLVEAARGFSDDVAERMRAVGGVPDARPQTVAASRIGDVGPDEIDTRACVEAIVALVRHTVDTIRRVHDPIDAEDPASADLLHAITLELEKQAWMIGSENRSPR 168
               SCOP domains d4a25a_ A: automated matches                                                                                                                                            SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhh...........eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4a25 A   2 TTIHDVQTTGLTQDAVTGFDASSRLNAGLQEVLVDLTALHLQGKQAHWNIVGENWRDLHLQLDTLVEAARGFSDDVAERMRAVGGVPDARPQTVAASRIGDVGPDEIDTRACVEAIVALVRHTVDTIRRVHDPIDAEDPASADLLHAITLELEKQAWMIGSENRSPR 168
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161

Chain B from PDB  Type:PROTEIN  Length:169
 aligned with A6WG04_KINRD | A6WG04 from UniProtKB/TrEMBL  Length:170

    Alignment length:169
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161         
         A6WG04_KINRD     2 TTIHDVQTTGLTQDAVTGFDASSRLNAGLQEVLVDLTALHLQGKQAHWNIVGENWRDLHLQLDTLVEAARGFSDDVAERMRAVGGVPDARPQTVAASRIGDVGPDEIDTRACVEAIVALVRHTVDTIRRVHDPIDAEDPASADLLHAITLELEKQAWMIGSENRSPRRR 170
               SCOP domains d4a25b_ B: automated matches                                                                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhh...........eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4a25 B   2 TTIHDVQTTGLTQDAVTGFDASSRLNAGLQEVLVDLTALHLQGKQAHWNIVGENWRDLHLQLDTLVEAARGFSDDVAERMRAVGGVPDARPQTVAASRIGDVGPDEIDTRACVEAIVALVRHTVDTIRRVHDPIDAEDPASADLLHAITLELEKQAWMIGSENRSPRRR 170
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161

Chain C from PDB  Type:PROTEIN  Length:169
 aligned with A6WG04_KINRD | A6WG04 from UniProtKB/TrEMBL  Length:170

    Alignment length:169
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161         
         A6WG04_KINRD     2 TTIHDVQTTGLTQDAVTGFDASSRLNAGLQEVLVDLTALHLQGKQAHWNIVGENWRDLHLQLDTLVEAARGFSDDVAERMRAVGGVPDARPQTVAASRIGDVGPDEIDTRACVEAIVALVRHTVDTIRRVHDPIDAEDPASADLLHAITLELEKQAWMIGSENRSPRRR 170
               SCOP domains d4a25c_ C: automated matches                                                                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhh...........eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4a25 C   2 TTIHDVQTTGLTQDAVTGFDASSRLNAGLQEVLVDLTALHLQGKQAHWNIVGENWRDLHLQLDTLVEAARGFSDDVAERMRAVGGVPDARPQTVAASRIGDVGPDEIDTRACVEAIVALVRHTVDTIRRVHDPIDAEDPASADLLHAITLELEKQAWMIGSENRSPRRR 170
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161

Chain D from PDB  Type:PROTEIN  Length:166
 aligned with A6WG04_KINRD | A6WG04 from UniProtKB/TrEMBL  Length:170

    Alignment length:166
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162      
         A6WG04_KINRD     3 TIHDVQTTGLTQDAVTGFDASSRLNAGLQEVLVDLTALHLQGKQAHWNIVGENWRDLHLQLDTLVEAARGFSDDVAERMRAVGGVPDARPQTVAASRIGDVGPDEIDTRACVEAIVALVRHTVDTIRRVHDPIDAEDPASADLLHAITLELEKQAWMIGSENRSPR 168
               SCOP domains d4a25d_ D: automated matches                                                                                                                                           SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhh...........eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4a25 D   3 TIHDVQTTGLTQDAVTGFDASSRLNAGLQEVLVDLTALHLQGKQAHWNIVGENWRDLHLQLDTLVEAARGFSDDVAERMRAVGGVPDARPQTVAASRIGDVGPDEIDTRACVEAIVALVRHTVDTIRRVHDPIDAEDPASADLLHAITLELEKQAWMIGSENRSPR 168
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
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	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Asymmetric Unit

Classes(

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Folds(

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Superfamilies( (-)

)

Families(

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Protein Domains( (-)

)

Organisms( (-)

)

Class: All alpha proteins (14657)

Fold: Ferritin-like (533)

Superfamily: Ferritin-like (489)

Family: automated matches (54)

Protein domain: automated matches (54)

Kineococcus radiotolerans [TaxId: 131568] (1)

1a	d4a25a_	A:
1b	d4a25b_	B:
1c	d4a25c_	C:
1d	d4a25d_	D:

(no "CATH Domain" information available for 4A25)

(no "Pfam Domain" information available for 4A25)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (A6WG04_KINRD | A6WG04)

molecular function
	GO:0008199	ferric iron binding	Interacting selectively and non-covalently with ferric iron, Fe(III).
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0016722	oxidoreductase activity, oxidizing metal ions	Catalysis of an oxidation-reduction in which the oxidation state of metal ion is altered.
biological process
	GO:0006879	cellular iron ion homeostasis	Any process involved in the maintenance of an internal steady state of iron ions at the level of a cell.
	GO:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
	GO:0006950	response to stress	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a disturbance in organismal or cellular homeostasis, usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation).
cellular component
	GO:0005623	cell	The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope.

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Biological Unit
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Description

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Ligands, Modified Residues, Ions (2, 16)

Sites (16, 16)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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